Correcting for bias of molecular confinement parameters induced by small-time-series sample sizes in single-molecule trajectories containing measurement noise

Physical Review E - Statistical, Nonlinear, and Soft Matter Physics

Volumn 88, Issue 1, 2013, Pages

  Calderon, Christopher P ^a  

^a NUMERICA CORPORATION   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EXPERIMENTAL OBSERVATION; MEAN SQUARE DISPLACEMENT; MOLECULAR CONFINEMENT; MULTIPLE NOISE SOURCES; PARAMETERS CHARACTERIZING; PRESENCE OF MEASUREMENT NOISE; SINGLE-MOLECULE STUDIES; SINGLE-PARTICLE TRACKING;

FENCES; IMPORTANCE SAMPLING; MOLECULES; PHOTONS; SPURIOUS SIGNAL NOISE;

SAMPLING;

ARTIFACT; CELLS; METABOLISM; STATISTICAL MODEL; THEORETICAL MODEL; TIME;

ARTIFACTS; CELLS; LIKELIHOOD FUNCTIONS; MODELS, THEORETICAL; TIME FACTORS;

EID: 84880614695     PISSN: 15393755     EISSN: 15502376     Source Type: Journal    
DOI: 10.1103/PhysRevE.88.012707     Document Type: Article

References (45)

1. J. Schlessinger, E. L. Elszon, W. W. Webb, I. Yahara, U. Rutishauser, and G. M. Edelman, Proc. Natl. Acad. Sci. USA PNASA6 0027-8424 10.1073/pnas.74.3. 1110 74, 1110 (1977).
2. Y. Sako, J. Cell Biol. JCLBA3 0021-9525 10.1083/jcb.125.6.1251 125, 1251 (1994).
3. A. Kusumi, C. Nakada, K. Ritchie, K. Murase, K. Suzuki, H. Murakoshi, R. S. Kasai, J. Kondo, and T. Fujiwara, Annu. Rev. Biophys. Biomol. Struct. ABBSE4 1056-8700 10.1146/annurev.biophys.34.040204.144637 34, 351 (2005).
4. I. Golding and E. C. Cox, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.96.098102 96, 098102 (2006).
5. N. Destainville and L. Salomé, Biophys. J. BIOJAU 0006-3495 10.1529/biophysj.105.075176 90, L17 (2006).
6. R. Rohatgi, L. Milenkovic, and M. P. Scott, Science SCIEAS 0036-8075 10.1126/science.1139740 317, 372 (2007).
7. M. J. Saxton, Biophys. J. BIOJAU 0006-3495 10.1529/biophysj.106.092619 92, 1178 (2007).
8. J. Masson, D. Casanova, S. Turkcan, G. Voisinne, M. Popoff, M. Vergassola, and A. Alexandrou, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.102.048103 102, 48103 (2009).
9. M. Magdziarz and J. Klafter, Phys. Rev. E PLEEE8 1539-3755 10.1103/PhysRevE.82.011129 82, 011129 (2010).
10. M. V. Nachury, E. S. Seeley, and H. Jin, Annu. Rev. Cell Dev. Biol. ARDBF8 1081-0706 10.1146/annurev.cellbio.042308.113337 26, 59 (2010).
11. H. Y. Park, A. R. Buxbaum, and R. H. Singer, Methods Enzymol. 9780-1237 10.1016/S0076-6879(10)72003-6 472, 387 (2010).
12. A. V. Weigel, B. Simon, M. M. Tamkun, and D. Krapf, Proc. Natl. Acad. Sci. USA PNASA6 0027-8424 10.1073/pnas.1016325108 108, 6438 (2011).
13. S. Türkcan, A. Alexandrou, and J.-B. Masson, Biophys. J. BIOJAU 0006-3495 10.1016/j.bpj.2012.01.063 102, 2288 (2012).
14. S. Y. Kim, Z. Gitai, A. Kinkhabwala, L. Shapiro, and W. E. Moerner, Proc. Nat. Acad. Sci. USA PNASA6 0027-8424 10.1073/pnas.0604503103 103, 10929 (2006).
15. S. Manley, J. M. Gillette, G. H. Patterson, H. Shroff, H. F. Hess, E. Betzig, and Lippincott-J. Schwartz, Nature Methods 1548-7091 10.1038/nmeth.1176 5, 155 (2008).
16. H. Qian, M. P. Sheetz, and E. L. Elson, Biophys. J. BIOJAU 0006-3495 10.1016/S0006-3495(91)82125-7 60, 910 (1991).
17. A. Kusumi, Y. Sako, and M. Yamamoto, Biophys. J. BIOJAU 0006-3495 10.1016/S0006-3495(93)81253-0 65, 2021 (1993).
18. A. van der Vaart, Asymptotic Statistics (Cambridge University Press, Cambridge, 1998).
19. R. J. Ober, S. Ram, and E. S. Ward, Biophys. J. BIOJAU 0006-3495 10.1016/S0006-3495(04)74193-4 86, 1185 (2004).
20. D. Montiel, H. Cang, and H. Yang, J. Phys. Chem. B JPCBFK 1520-6106 10.1021/jp062024j 110, 19763 (2006).
21. C. P. Calderon, Multiscale Model. Simul. 1540-3459 10.1137/050643647 6, 656 (2007).
22. A. J. Berglund, Phys. Rev. E PLEEE8 1539-3755 10.1103/PhysRevE.82.011917 82, 011917 (2010).
23. X. Michalet and A. J. Berglund, Phys. Rev. E PLEEE8 1539-3755 10.1103/PhysRevE.85.061916 85, 061916 (2012).
24. M. A. Thompson, J. M. Casolari, M. Badieirostami, P. O. Brown, and W. E. Moerner, Proc. Natl. Acad. Sci. USA PNASA6 0027-8424 10.1073/pnas.1012868107 107, 17864 (2010).
25. C. P. Calderon, W. Chen, N. Harris, K. Lin, and C. Kiang, J. Phys.: Condens. Matter JCOMEL 0953-8984 10.1088/0953-8984/21/3/034114 21, 034114 (2009).
26. C. P. Calderon, N. Harris, C. Kiang, and D. Cox, J. Phys. Chem. B JPCBFK 1520-6106 10.1021/jp807908c 113, 138 (2009).
27. C. P. Calderon, J. Phys. Chem. B JPCBFK 1520-6106 10.1021/jp911124z 114, 3242 (2010).
28. J. Hamilton, Time Series Analysis (Princeton University Press, Princeton, NJ, 1994).
29. A. Shiriaev and Y. Spokoiny, Statistical Experiments and Decisions: Asymptotic Theory (World Scientific, Singapore, 1999).
30. C. Y. Tang and S. X. Chen, J. Econometrics 0304-4076 10.1016/j.jeconom. 2008.11.001 149, 65 (2009).
31. L. Zhang, P. A. Mykland, and Y. Ait-Sahalia, J. Am. Stat. Assoc. JSTNAL 0162-1459 10.1198/016214505000000169 100, 1394 (2005).
32. Y. Aït-Sahalia, J. Fan, and D. Xiu, J. Am. Stat. Assoc. JSTNAL 0162-1459 10.1198/jasa.2010.tm10163 105, 1504 (2010).
33. C. P. Calderon, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.2567098 126, 084106 (2007).
34. C. P. Calderon and K. Arora, J. Chem. Theory Comput. 1549-9618 10.1021/ct800282a 5, 47 (2009).
35. C. P. Calderon, J. Martinez, R. Carroll, and D. Sorensen, Multiscale Model. Simul. 1540-3459 10.1137/090768102 8, 1562 (2010).
36. C. P. Calderon, N. Harris, C. Kiang, and D. Cox, J. Mol. Recognit. 0952-3499 10.1002/jmr.959 22, 356 (2009).
37. H. Risken, The Fokker-Planck Equation (Springer-Verlag, Berlin, 1996).
38. Y. Hong and H. Li, Rev. Financ. Stud. 1465-7368 10.1093/rfs/hhh006 18, 37 (2005).
39. A. Lubelski, I. M. Sokolov, and J. Klafter, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.100.250602 100, 250602 (2008).
40. R. Yokoyama, Probab. Theory Relat. Fields 52, 45 (1980).
41. P. Billingsley, Convergence of Probability Measures (Wiley, New York, 1968).
42. A. Davison and D. Hinkley, Bootstrap Methods and Their Application, Cambridge Series in Statistical and Probabilistic Mathematics (Cambridge University Press, Cambridge, 1997).
43. A. Koutris, M. S. Heracleous, and A. Spanos, Econometric Rev. 0747-4938 10.1080/07474930801959776 27, 363 (2008).
44. H. V. Poor and O. Hadjiliadis, Quickest Detection (Cambridge University Press, Cambridge, 2008).
45. P. Kloeden and E. Platen, Numerical Solution of Stochastic Differential Equations (Springer-Verlag, Berlin, 1992).